even if you have loaded your os in D: drive, there are files" BOOT.ini, ntdetect.com, ntldr. " this three files in C: drive, helps to boot your os in D: drive.
if you format C: drive, you will not able to boot your D: drive os.
first copy this three files on another drive. boot with bootable cd/floppy, in command prompt type "format c:" . after format is completed, copy those three files back to C: drive.